Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_010876437.1 MTH_RS03770 aspartate kinase
Query= BRENDA::Q9WZ17 (739 letters) >NCBI__GCF_000008645.1:WP_010876437.1 Length = 406 Score = 166 bits (421), Expect = 2e-45 Identities = 123/410 (30%), Positives = 215/410 (52%), Gaps = 27/410 (6%) Query: 340 VVVMKFGGAAISDVEKLEKVAEKIIKRKKSGVKPVVVLSAMGDTTDHLIELA-KTIDENP 398 ++V KFGG +I + +++K A ++K G K VVV+SA+ TTD L+++ + +++ Sbjct: 3 LIVAKFGGTSIGNGRRIKKAARSVVKEYMKGRKVVVVVSAINKTTDELLQIVDEAMEDAV 62 Query: 399 DPRELDLLLSTGEIQSVALMSIALRKRGYKA--ISFTGNQLKIITDKRYGSARIIDINTD 456 ++L ++S GE+ SV + S A+ G K+ I ++ IITD +A++ T+ Sbjct: 63 TEKQLAEIVSMGEMTSVRIFSSAIEALGVKSEYIDPFMDEWPIITDSNLLNAKVDFEATE 122 Query: 457 IISR----YLKQDFIPVVAGFQGITETGDITTLGRGGSDLTAIALAYSLGADLCELYKDV 512 SR L Q IPVV GF G G ITTLGRGGSD+TA L + L AD + DV Sbjct: 123 EKSRELLKLLDQGIIPVVCGFLGRDPNGYITTLGRGGSDITAFLLGHCLKADEVIIVTDV 182 Query: 513 DGVYTADPRIVKDARVIKELSWEEMIELSRHGAQVLQARAAEFARKYGVKVLIKNAHKET 572 GV + DP ++ A+ + ++S EEM +L+ HGAQVL A ++ +I H Sbjct: 183 GGVMSTDPNKLQGAKKLDKISVEEMRDLATHGAQVLHPHALKYKDPDIKAKIIGFEH--- 239 Query: 573 RGTLIWEGTKV----ENPIVRAVTFED---GMAKVVLKDVPDKPGVAARIMRTLSQMGVN 625 G L GT++ +N +V+ T + VV + + +KPG+ AR+ L++ +N Sbjct: 240 -GDLSAPGTEIIGPSKNKMVKTTTLNPDPISVVAVVGEKILNKPGILARLTSRLAENSIN 298 Query: 626 IDMIIQGMKSGEYNTVAFIVPE--SQLGKLDIDLLKTRSEAKEIIIEKGLAKVSIVGVNL 683 I G+ +G+ + F+ + + +L D++ + + + + +A ++I + Sbjct: 299 ----IIGISTGQNSVTIFVDKKDADEAHRLLHDVVIADDDLSSLSLGRDIAMITISSPDF 354 Query: 684 TSTPEISATLFETLANEGINIDMISASSSRISVII---DGKYVEDAVKAI 730 TP I + + + L + +NI IS+S + + + + DGK + V+ + Sbjct: 355 IDTPGIISEITKPLRDNDLNIVEISSSQTSVVIFVDWNDGKKAYELVRGV 404 Lambda K H 0.318 0.137 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 662 Number of extensions: 31 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 739 Length of database: 406 Length adjustment: 35 Effective length of query: 704 Effective length of database: 371 Effective search space: 261184 Effective search space used: 261184 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory